Secret File
by MarionTheEvilLibrarian
Summary: When Thor realizes Loki hasn't been acting himself but has been possessed by the Chitauri - what will he do? Can Loki be forgiven for what he has done - if in fact he did it at all or will he be subject to inprisonment and torture for his misdeeds? The Avengers are torn between punishment or a gentler form of rehabilitation and everything is falling apart for Loki - rapidly.
1. It's Just The Beginning

_Secret File:_

_ Amanda's Fanfic_

An enormous clang resounded off the top of the Stark tower and mixed in with the rest of the screams of horror and explosions happening across the city as the Avengers tried to beat back Loki's apparent army. The Avengers were hopelessly outnumbered and were getting tired as the Chitauri poured endlessly out of the portal that Loki had created with the help of the Tesseract. The S.H.I.E.L.D. board was already threatening to destroy the whole city with a nuclear blast and hope that it would close the portal as well but the Avengers weren't having it: it would kill too many innocent people.

Loki, meanwhile, was atop the Stark tower fighting the other divine deity; his half-brother, Thor. Thor was desperately trying not to kill Loki – only to subdue him so he could take him, the Tesseract, and hopefully Jane back to Asgard and knock some sense into Loki there. It was here that Thor finally realized what had been bothering him about Loki, something that had seemed fundamentally off since the first time he had seen him alive on this planet: his eyes were ice blue like Clint's had been when Loki had had control over him. Thor was so surprised that he hadn't noticed this earlier that Loki hit him across the face before he recovered and even then all he did was grab Loki's shoulders and shake him violently saying, "Loki! Brother! You have to fight this Loki! It's me brother, it's your brother Thor!"

"I have no brother!" Loki growled back angrily. He shook himself out of Thor's grip and lashed out at him with his staff and thwacking him once again in the head. This time it seemed to do the trick, though, and something clicked in Thor's mind: when Clint had been possessed Agent Romanoff had done nothing more than literally knock the sense back into him. If Romanoff could beat the possession out of Clint he could do the same to Loki.

Thor swung at Loki's head but Loki blocked it easily and rushed forward to attack Thor but Thor swung again – this time more out of self-preservation and panic than anything else – and his fist hit Loki's temple a lot harder than he had meant.

Loki crumpled to the ground but he wasn't finished yet, it seemed. Loki tried to get up but fell back again, unconscious. Luckily it was just enough time for Thor to see that Loki's eyes were emerald green again, as they should be.

Thor walked cautiously to Loki's side and reached down to pick him up when he noticed Loki was bleeding heavily from his nose and little trails of blood were dripping out from under his eyelids. Thor froze halfway to the ground in shock: something had definitely gone terribly wrong.

Just then Tony Stark landed on the roof ten feet away with his hand raised ready to blast Loki to oblivion but Thor managed to shake himself back to reality to warn him off before anything seriously bad happened.

Tony knew right away something was wrong and, even though he would never admit it to anyone, he had a little respect for the god so he was a little concerned when Thor knelt to the ground to cradle the slender, black haired god's head in his lap. When he saw all the blood pouring off Loki's face he couldn't bite back the comment fast enough and said, "God, how hard did you hit him?"

"This isn't the time for jokes, Stark, and Loki doesn't have the time for us to sit here and wait for me to explain. He needs a healer – now!" With that Thor picked Loki up as gently as he could and told Stark to get the best doctors available as he walked down the building.

"Wait! Just because he's unconscious doesn't mean he isn't a threat anymore, Thor. The war is still on: the beasts haven't stopped coming in case you haven't noticed," Tony said waving his hands at the city.

Thor ignored Tony completely and made his way off the roof.

Just then Fury's voice crackled in Tony's ear, "_Tony. A nuclear bomb is flying straight at the city as we speak, the portal is still open, and all of you will die if you don't do something about it _now!"

Then, before Tony could respond Natasha interrupted, "_Guys! I can close the portal _right now!" Her voice was rough from battle, anxiety, and exhaustion but she sounded positive. Something about how both comments had been made right after each other made something click in Tony's mind.

"Natasha, don't close it just yet – I know what we have to do about the bomb and the aliens. Everyone else; keep fighting!"

Tony flew towards the missile and started directing it toward the portal. "_Tony, be careful!" _Captain America yelled at him. "_If this doesn't work –"_

"Yeah, yeah, I get it: I go boom, too," Tony interrupted, annoyed. It was already hard enough to make himself do the right thing, but adding all the negatives on it was really putting a damper on his mood.

Tony pushed up against the underside of the large, and very dangerous, missile. It was arcing up rapidly and he knew he was going to have to go through the portal with the missile and his mind started racing, trying to find a better solution. Natasha would have to close the portal before the bomb exploded because otherwise the explosion would just travel through, but if Tony didn't make it back before she closed it – well; he hadn't tested the armor for durability against nuclear blasts yet.

Tony was seconds away from the portal and knew there was no way out of this one. He flew through the portal with the bomb and let it fly toward the Chitauri's planet. Tony tried to get back to the portal but his blasters had already frozen up and his oxygen levels were dipping dangerously near zero. Tony gasped as the oxygen totally dissipated and the suit started floating freely through space. He forced his eyes to stay open and make sure the bomb blasted the Chitauri planet to tiny alien bits but his vision was narrowing to a point rather rapidly.

Back on earth Captain America was yelling through his mouth piece, "TONY! Get back down here, NOW!" He watched through the portal as the bomb exploded and knew they had to close the portal with Tony still inside of it. "Natasha, close the portal."

No one spoke on Natasha's end, she just gave the Captain a grim nod but everyone else started protesting, "We can wait a few more seconds!" Clint yelled, even as he shot more Chitauri out of the sky.

"NO! Don't wait Natasha. Do it now!" Captain America yelled. Through the portal he could still see the bomb slowly creeping toward the opening but he could also see the Ironman suit being pushed back towards the hole by the force of the blast. "Do you see that? COME ON TONY, GET DOWN HERE!"

Just as the portal closed the Ironman suit slipped through and started falling towards earth. "What's wrong?" Clint asked as he watched the suit fall. "He's not slowing down – why isn't he slowing down?"

The Hulk roared and started racing towards Tony, leaping from building to building and just catching Tony before dropping him in front of Hawkeye and Captain America who promptly tore off Tony's helmet and leaned down to listen for his breath. He shook his head – there wasn't any.

Everyone stared in horror at Tony's prone body, not even noticing that all the aliens had died as soon as the bomb went off. The Hulk broke the silence with a loud roar of grief. Suddenly Tony's head shot up at the sound and said, "What I miss?" gasping.

"Hold on Loki, I can fix this…" Thor said as he carried Loki down the Stark tower as gently as he could. He kept murmuring the reassuring, useless words as he hoped Loki would just open his eyes. He didn't open his eyes or say a single thing. The only noise Loki made was a hollow rattling as he breathed.

Thor sat outside of Loki's hospital room with his head in his hands. The doctors had confirmed that Loki had a severe concussion but the way the doctor said it had piqued Thor's interest. _"What else?"_ he had asked.

"_We're not entirely sure. We were monitoring his brain activity – which was a little confused, but this is normal for a concussion this bad but it was…unbalanced. His brain would suddenly have high spikes of activity and then it would mellow out to nearly nothing at all. I… I don't know what else to do for him."_

That was yesterday.

Now he was just sitting on a bench outside of Loki's room worrying. The healers on this planet were pathetic compared to those of Asgard. Loki could have been healed by now if they had gone to Asgard but S.H.I.E.L.D. had insisted that Loki and Thor stay here. Now Agent Fury had called a meeting but Thor had refused to move from this spot so Fury, Coulsen, and the rest of the Avengers had agreed to meet here.

"I don't understand," Steve Rogers, A.K.A. Captain America, said as he walked in. "Why did you beat your brother to death if you were only going to bring him to a hospital in the end?"

Thor was about to respond when Natasha walked in, "Save it until the rest come, Thor," she said shortly.

So he did: Tony Stark and Bruce Banner walked in next with Fury and Coulsen on their heels. Clint strode in last and Thor began his story.

"When we were fighting on the roof I realized that Loki hadn't been acting his self this whole time and that his eyes were ice blue, like yours were," he said motioning at Hawkeye who looked at the ground and shrugged. "I then remembered what Natasha had said about recalibrating Clint's brain –"

"Literally knocking the sense back into him," Tony said with a satisfied grin and nod.

"Yes, well, that plan went decidedly south and now we're here," Thor said with a heavy sigh.

"You shouldn't have brought him here, Thor; he's a danger to earth and to himself. You should have just destroyed him," Fury said with a frustrated glint in his eye.

Thor shot up angrily and said, "He is my brother! He was unable to control his actions! He shouldn't have to pay for this."

"How do we know the Chitauri won't inhabit his mind again?" Fury countered.

"I'll take him back to Asgard," Thor said just as quickly.

"Thor," Clint said quickly and interrupting Fury's retort. He put his hand on Thor's shoulder, "You know you don't have the power to get back to Asgard."

"Together –" Thor began as he sunk back into his chair realizing there wasn't a way out of this for Loki.

"Thor, even if you could go back we would need you here in case the Chitauri found a way to come back here." Thor didn't know who had said it but he nodded, knowing it was completely true. His blood was pounding in his ears and his eyes were stinging. No matter what Loki had done he was still his brother and he loved him – even if Loki was a Frost Giant. He just wanted Loki to be safe. He wanted whatever was possessing Loki to leave and when it did he was going to have the Chitauri face the wrath of a god.

He snapped back to reality when he heard a groan from Loki's room. He crept into his room, not even noticing that nearly everyone had left accept for Bruce who came in behind him.

Loki's head was tilted towards the door and his face was twisted in an expression of pain even unconscious. His skin was pale and drawn and a large bruise was filling in where Thor had hit him. "The doctor just left. You hit him pretty hard – be glad he's immortal," Bruce said as he left.

Thor sighed and pulled a chair over to Loki's bed. There were so many things Thor wanted to say – if only Loki would wake up! He would convince him that it doesn't matter if Loki's a Frost Giant: he's still his brother. He would apologize for hitting him so unnecessarily hard.

His thinking was interrupted when Tony walked in with his arms loaded with food from the hospital vending machine down the hall. _How typical of Stark. _Thor thought. Tony really was an inconsiderate, vulgar, and introverted man. How did anyone stand him?

Tony just sat down, oblivious to Thor's train of thought, and asked "Did he wake up yet?"

_As if you care, _Thor wanted to say but just then Loki's eyes snapped open and he gasped. His eyes tried to focus on Thor but they were foggy with pain and exhaustion and his pupils were largely dilated. Loki whispered something and Thor knelt next to his head and said, "Loki, I'm so sorry."

Tony wanted to bolt out of the room – he wasn't good at…emotions. Instead he walked closer to Thor and saw that there was a track of tears running down the god of thunder's face. He had never seen the god cry and he felt terrible because he couldn't do anything about it. Before he could do anything ridiculous, like cry, he left the room. He was so desperate to get out of the sterile, unfeeling hospital that he didn't even notice Natasha and Fury talking outside in the hall.

"What's wrong with Stark?" Natasha wondered aloud as he dashed by.

"There are too many things to say to that," Fury said with a dismissive wave of his hand. "As I was saying: we can't kill Loki anymore, nor can we send him back."

"Thor could easily watch after him," Romanoff said.

"Do we really want the god who tried to kill his brother being babysat by said brother? And according to the Norse legends Loki has been easily escaping Thor and Odin for his whole life. It wouldn't work," Fury said with finality.

"What else can we do?" Romanoff asked. Fury shrugged and Natasha glanced into the room where Thor was still kneeling by Loki. He looked up at Natasha but she shifted her gaze back to Fury. "Do you want to tell him we won't be killing Loki, or shall I?" She said it completely calmly but Fury knew she meant it as a small joke when she smirked at the very idea of trying to kill a god.

Thor and Hawkeye were helping Loki into a S.H.I.E.L.D. van when they realized that Tony was nowhere to be found but Fury told everyone to keep moving without him.

Fury had decided it would be best to keep an eye on Loki at S.H.I.E.L.D. headquarters and Thor, still immensely depressed, could do nothing but agree. Fury wanted all the Avengers to convene at headquarters anyway and they could give Loki equally good medical care there. Loki was fully awake now, if slightly unfocused, but couldn't walk without help. He went along with the Avengers willingly but he was being eerily quiet the whole way.

When they finally got the pale god into the van he rested his head back, trying not to pass out. Even though he was better he still let out a sharp gasp of pain every time they hit a bump in the road.

When they reached the building Loki literally didn't even have the energy to lift his head. Clint and Steve were going to assist Loki but when they saw how bad he looked they realized he wouldn't be walking for a while. When Thor got out of the van and saw Loki he quickly scooped him up and brought him inside.

**End of Part One**


	2. Handles Situation Very Carefully

**Secret File**

** Part Two**

Thor carried Loki as carefully as humanly – and godly – possible into the S.H.I.E.L.D. building and followed Fury as he led him down the confusing maze of tunnels to a room with what looked like the glass holding cell that had been made for the Hulk on the flying version of S.H.I.E.L.D. The cell was completely bare except a plain white bed which Thor gently laid Loki onto. There was nothing Loki could do but clench his teeth against the pain and try to muffle his groans.

Thor looked around the holding cell and couldn't help thinking; _He would have been treated much better in Asgard. _ Loki hadn't even moved after Thor had set him down and as Thor gazed down at the broken form of his younger brother he saw Loki clenching his fists and jaw as a single tear slid down his cheek. What else could he do? He wanted to help his brother as much as he could but Thor had never been a healer and wasn't going to risk trying it out on Loki so when Fury motioned for Thor to follow him out of the room all Thor could do was send a silent prayer to Odin and hope he had heard.

Loki could barely open his eyes without the brightness of the room sending shoots of pain into his brain and down his spine which settled in his stomach making him nauseous. He clenched his whole body against the pain hoping it would fade but as Loki watched Thor turn away a whole other pain bloomed inside of his chest. _Of course_ Thor was just leaving him. Loki always had been the black sheep of the family. Ever since he was little Loki had been looked down upon by his brother. And now, even here in this unfamiliar place, Thor was leaving him behind.

_Loki remembered being on the Rainbow Bridge with Thor and Odin and all he could think of was how he wanted to get away. He didn't want to be near the people who constantly looked down on him from childhood on. At least he knew why they had hated him so much: he was a Frost Giant. He had been and always would be viewed as an inconvenience. So, in his mind, it made perfect sense that the only way to get away would be to just… let go. _

_He remembered Thor screaming his name as if Thor actually cared if he survived or not and he remembered turning his back on them as he fell, facing what was new. He remembered falling down, down, down and not even caring where he ended up. He wanted to die. There was no place for him in this universe: he couldn't be trusted in Asgard, and he was hated in Jotunheim now that he had killed Laufey. There was no place for him. _

_He remembered glaring down defiantly at the black and broken looking planet rushing up to meet him. Somewhere, in the back of his mind, he realized that this was definitely not one of the nine planets but, again, he didn't care. He would let his death come and he would embrace his end gratefully. _

_He remembered the last few seconds before he hit the ground. He remembered the panic and fear of death creeping into him now but he fought it back as he harshly reminded himself that there was no place for him anyway. _

_He remembered the instant pain that came like a giant wave crashing against his whole body all at once. He felt like everything was broken. Why couldn't he have had the good fortune of dying instantly? He had landed on his side with his arm underneath him which was now definitely broken. In the split second before hitting the ground his body had reacted and tried to move but it was too late and now he lay there, wishing death would just come. The pain was constant and seemed to grow and multiply with every passing second. Soon it was too much and, to protect itself, Loki's brain shut off and he slid into unconsciousness. _

_Unfortunately this oblivion hadn't lasted long: he had moments of lucidity as he heard people – no, things – moving around him. It felt like every time they even merely brushed his totally destroyed and abused body that they were pounding on him with mjolnir itself. He could hear himself screaming and cursing them but it was like it wasn't him who was doing it. He was in a completely different world – one where there was nothing but an oppressive haze of pain that smothered everything else from reality into oblivion. _

_These moments happened too often for his liking and when he finally woke up – not just delirious or choked with hallucinations as he had been before, but really awake – he could barely move without causing himself more than the constant amount of pain. He put all his energy in just staying awake for at least a few minutes as he observed the room he was in. It was very dark and therefore there wasn't much he could see but as his eyes adjusted his eyes caught sight of what must have been the outline of the door. It was oddly shaped and looked very thick and metallic. He wanted so desperately to figure out where he was but he was so tired. Even if he had just been sleeping for weeks he was still tired._

_The last thing he did before falling asleep was to take stock of his injuries. Right arm: broken. Left hand: broken. Ribs: quite a few broken. He slowly and painfully brought a hand to his chest and felt how broken and swollen from internal bleeding it was. He slowly dragged the same hand up to his face and found that nothing was broken but as his hand reached the side of his head he found it covered in a large amount of bandaging. His left knee felt sore as if it had been wrenched from its socket and then popped back in. He gritted his teeth as he gingerly laid his arm back down. Suddenly a sharp jab of pain ran across his chest and he sucked in a large breath which subsequently caused more pain throughout his body and he passed out. _

_He remembered waking up later with a burning determination to just die. Looking at his life so far: what had he accomplished? What was left for him? He had tried to keep disaster from coming to Asgard by manipulating Odin to banish Thor but that turned into a large disaster and he had not only failed Odin but he ruined his chances of even being accepted into Jotunheim. He figured that it would just be for the best. _

_Later on, when the strange creatures of the planet came in to treat his wounds again he spotted one of them carrying a large tray of medical supplies. Surely one of the bottles had something deadly if taken in large amounts – even to him. After all; it would take powerful drugs to just treat him, therefore they were probably already shooting large amounts into him anyway. It shouldn't take much more._

_By the time the creatures had left he had successfully swiped a bottle from them without their notice. After multiple tries – he only had use of one hand – he opened the stupid bottle and poured ten of the translucent grey pills into his hand. Before he could talk himself out of it he threw them back and closed his eyes and waited. _

_Loki had gotten extremely lucky and couldn't have picked a better bottle to swipe: the pills were evidently pain killers and before he could even hide the bottle his body lost all feeling. Just before he closed his eyes the door banged open and several of the creatures burst into the room. One grabbed him by the shoulders and hauled him up in a manner that should have been extremely painful. Another grabbed his face and started hissing some weird language and he lost conscious thought._

_He woke up later laying on top of a tall tower in some unknown place with Thor running towards him. Even here, in death, Thor had come to mock him, to remind him of his failures against Odin. _

When Thor had turned to leave him here in this unfamiliar place Loki was utterly spent. There was nothing more left in him. A single tear slid down his cheek as he drifted into unconsciousness.


	3. Conspiracy Theories

Fury's lone eye looked around the room in its perpetual scowl as he decided how he should talk his way through the minefield that is Thor. Thor, himself, was sitting at one end of the table with his head bowed and elbows propped up on the table with his hands folded as if he were deep in prayer. Fury knew Thor was in strong disagreement with SHIELD and their decision to keep Loki and Thor here for the time being, so, the trick would be to get to the part of how they're sending them home before Thor exploded.

_Maybe I could get some support from the others, _Fury thought half hopefully, half sarcastically. Nevertheless he looked towards Bruce Banner whose eyes where wandering the room as if he were waiting for some_thing _to happen at any moment. If anyone, he would be the one to support Fury. He had the most analytical and logical mind among the Avengers and would most definitely see the benefit of keeping Loki around for the past 24 hours. But he would also realize the risk of Loki's health here, where they could offer no help to Loki's psychological state. After all, Loki hadn't even awoken from his comatose state yet.

He glanced towards Agent Romanoff who was looking around expectantly and unemotional as ever. She was a good Agent and would help him with Thor if he ordered her to – but he really didn't want to order support. Despite her tough exterior she did have her weaknesses and compassions. Deep inside – deep, deep down – she was probably feeling for Loki and Thor.

So those two options were out, but he really, really, really didn't want to do this without any support. Luckily there was still… Hawkeye… He disregarded that thought immediately. Hawkeye probably hated Loki's guts after what he had done to him. But who was he to say? It's not like Fury and Hawkeye were good friends.

After Fury thought _that _he _knew _he was grasping at straws.

Well, maybe – just maybe – Steve Rogers would understand. Steve was exceedingly compassionate and understanding about things – if a little naïve. But he did have a strong sense of justice…which would be exactly why he wouldn't defend Fury for keeping Loki here. It appeared as if Loki really had no recollection of his past deeds on earth whatsoever which made him…innocent. But there were real reasons he was being kept here they...they were just hard for him and the rest of the Avengers to accept.

Well, it looked as if Fury would be doing this alone after all. "Loki is slowly improving," Fury started cautiously as he kept his eye on Thor. "And we have controlled the Tesseract well enough to send Thor and Loki back to Asgard." He watched Thor but he didn't respond in any way. "Thor, you and Loki could go back within three days."

That was it. Thor exploded, "Three days? My brother needed to be in Asgard yesterday." He shook his shaggy blond hair angrily, "Your earthly doctors are doing _nothing _for him here! He needs a healer from Asgard and instead he is left in a – in a cage! He is being watched day and night in case he attacks you even though he is clearly unwell! He. Was. Possessed! Can you not understand that?"

"Do not forget that Loki is still a threa–" Fury said as he received the expected onslaught.

"Oh, give the guy a break, Fury. He almost killed his thought-to-be evil brother two days ago before finding out that he was being possessed by creepy, evil aliens," Hawkeye said with a glare.

_Well now I know _he's_ not going to support me._ Fury thought. It really had seemed as if Hawkeye had truly forgiven Loki for his own possession. "I understand that, but that does not mean that they won't possess him again and turn him into their own personal flying monkey."

"I don't understa–" Thor started.

"I understood!" Steve said putting his hand up like a school kid. He looked around: Hawkeye was giving Fury a confused look. Romanoff didn't look any more knowledgeable about the reference either. "I understood that reference."

X+X+X+X+X+X

After Rogers proudly made it clear that he finally understood a reference Fury concluded the meeting and left the room with an irate Thor right on his heels. The rest of the team stayed in the room each stuck in their own contemplative world. What should they do about Loki? It was clear what Thor thought was necessary… And even though the whole team agreed with Thor they also knew that they couldn't very well disobey Fury outright. They would have to somehow appease Fury and Thor _and _do what was still best for Loki's health. Out of the silence Bruce spoke up, "It would seem that we are stuck."

"You think?" Clint said, frustrated. "I don't know about you guys but I really would rather have both Fury _and _Thor on my side at all times."

"We need to find a common ground for them to agree upon," Bruce said as he turned his contemplative gaze toward the window. The sun was setting and it cast the whole city into flame. It looked magnificent. And broken. "We could move Loki to a more accommodating location," He mused.

Romanoff nodded but also saw the flaws, "Where would _that_ be?"

Just then, like a sign from heaven, Tony walked in the room. He glanced around the room – even though he was wearing sunglasses everyone knew he was wearing his signature "Snark Stark Smirk". He walked towards the table and, very unceremoniously, flopped into a seat. He smiled playfully and looked around the table, "Are you guys…having a meeting…without _me?"_ He asked as he put his hand to his heart in mock hurt and exasperation. Steve, who had not said anything since the monkeys dropped his head into his hands. Steve had had respect for Tony's father but how had Tony come about being…Tony?

Bruce explained to Tony how Thor just went on a rant about his brother and how it would be a good idea to move him to a place more comfortable then HQ. Then, without hesitation, Tony suggested, "He could come to Stark Towers."

Romanoff replied "Are you sure you want a delicate god," she looked around to make sure Thor was nowhere near, "and possibly a threat in your house? And his brother probably breathing down your neck?"

Tony smirked "Of course, I need something to keep me on my toes. Plus, I get to brag I took care of a Norse god who tried to take over the world. Who wouldn't want that?" He pulled up a chair and relined in it with his feet on the table.

Romanoff was getting slightly irritated at this, "Stark, you know this is big deal, you cannot mess up, and if you do, Thor will have your head"

Tony just replied "Wonderful! So," he rose from his chair "I'll just take him, any objections?" and started to leave, but before he reached the door

Romanoff said, with a stern tone even though you could hear the anger build up "You can't just take him and walk out, he is still in critical condition."

"Why can't I? I'm _Tony Stark" _

"Because you can kill him!"

"Really? Me, killing an immortal god by taking him away from this prison? Yes, because I'm sure that he is going to resist and fight back" he paused "Where's Thor, he will be on my side"

Clint piped up "He got angered and left, we don't know where he went, but I'm sure he didn't go far"

Tony glared at Romanoff "Oh look! Barton is on my side too! What about you Cap?"

Steve pulled his head out of his hands and replied "You can't just pick him up and go, he can barely walk... but I agree with the idea of him recovering at Stark tower"

"4 against 1, I win." With that he left the room and walked down the hallway to where Loki was being held.


End file.
